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att / rcloud

Collaborative data analysis and visualization
http://rcloud.social
MIT License
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Installation issues with Rcloud app #2710

Closed sunny143code closed 4 years ago

sunny143code commented 4 years ago

Hi @gordonwoodhull, Thanks for all your help. I am still receiving the below errors after I installed all the package shown below so could you help if you know anything about it.

 --- Installing RCloud packages and dependencies in R
Warning: unable to access index for repository http://r.research.att.com/src/con                                                                                                             trib:
  cannot open URL 'http://r.research.att.com/src/contrib/PACKAGES'
Warning: dependencies 'Rcpp', 'httr', 'reticulate', 'jsonlite', 'rmarkdown', 'rj                                                                                                             son', 'RCurl', 'sendmailR', 'stringr', 'BH', 'Rook', 'yaml', 'xfun' are not avai                                                                                                             lable
also installing the dependencies 'evaluate', 'highr', 'guitar', 'PKI', 'github',                                                                                                              'RSclient', 'FastRWeb', 'knitr', 'markdown', 'Rserve', 'base64enc', 'uuid', 'un                                                                                                             ixtools', 'rediscc', 'png', 'Cairo', 'mime'

trying URL 'http://rforge.net/src/contrib/evaluate_0.13.2.tar.gz'
Content type 'application/x-gzip' length 21484 bytes (20 KB)
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downloaded 20 KB
trying URL 'http://rforge.net/src/contrib/highr_0.8.1.tar.gz'
Content type 'application/x-gzip' length 16514 bytes (16 KB)
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downloaded 16 KB
trying URL 'http://rforge.net/src/contrib/guitar_0.0.3.1.tar.gz'
Content type 'application/x-gzip' length 726256 bytes (709 KB)
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downloaded 709 KB
trying URL 'http://rforge.net/src/contrib/PKI_0.1-5.tar.gz'
Content type 'application/x-gzip' length 68047 bytes (66 KB)
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downloaded 66 KB
trying URL 'http://rforge.net/src/contrib/github_0.9.9.tar.gz'
Content type 'application/x-gzip' length 32747 bytes (31 KB)
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downloaded 31 KB
trying URL 'http://rforge.net/src/contrib/RSclient_0.7-5.tar.gz'
Content type 'application/x-gzip' length 38846 bytes (37 KB)
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downloaded 37 KB
trying URL 'http://rforge.net/src/contrib/FastRWeb_1.1-2.tar.gz'
Content type 'application/x-gzip' length 80449 bytes (78 KB)
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downloaded 78 KB
trying URL 'http://rforge.net/src/contrib/knitr_1.18.10.tar.gz'
Content type 'application/x-gzip' length 316349 bytes (308 KB)
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downloaded 308 KB
trying URL 'http://rforge.net/src/contrib/markdown_1.1.1.tar.gz'
Content type 'application/x-gzip' length 88420 bytes (86 KB)
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downloaded 86 KB
trying URL 'http://rforge.net/src/contrib/Rserve_1.8-6.tar.gz'
Content type 'application/x-gzip' length 497894 bytes (486 KB)
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downloaded 486 KB
trying URL 'http://rforge.net/src/contrib/base64enc_0.1-4.tar.gz'
Content type 'application/x-gzip' length 7265 bytes
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downloaded 7265 bytes
trying URL 'http://rforge.net/src/contrib/uuid_0.1-2.tar.gz'
Content type 'application/x-gzip' length 45927 bytes (44 KB)
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downloaded 44 KB
trying URL 'http://rforge.net/src/contrib/unixtools_0.1-1.tar.gz'
Content type 'application/x-gzip' length 4825 bytes
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downloaded 4825 bytes
trying URL 'http://rforge.net/src/contrib/rediscc_0.1-5.tar.gz'
Content type 'application/x-gzip' length 34918 bytes (34 KB)
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downloaded 34 KB
trying URL 'http://rforge.net/src/contrib/png_0.1-8.tar.gz'
Content type 'application/x-gzip' length 24806 bytes (24 KB)
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downloaded 24 KB
trying URL 'http://rforge.net/src/contrib/Cairo_1.5-11.tar.gz'
Content type 'application/x-gzip' length 84451 bytes (82 KB)
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downloaded 82 KB
trying URL 'http://rforge.net/src/contrib/mime_0.8.1.tar.gz'
Content type 'application/x-gzip' length 12192 bytes (11 KB)
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downloaded 11 KB
* installing *source* package 'evaluate' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (evaluate)
* installing *source* package 'highr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (highr)
ERROR: dependencies 'Rcpp', 'stringr', 'BH' are not available for package 'guita                                                                                                             r'
* removing '/opt/R/3.6.1/lib/R/library/guitar'
ERROR: dependencies 'httr', 'Rook', 'stringr', 'jsonlite' are not available for                                                                                                              package 'github'
* removing '/opt/R/3.6.1/lib/R/library/github'
* installing *source* package 'RSclient' ...
** using staged installation
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c cli.c -o cli.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c qap_decode.c -o qap_decode.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c qap_encode.c -o qap_encode.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o RSclient.so cli.o qap_d                                                                                                             ecode.o qap_encode.o -lssl -L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-RSclient/00new/RSclient/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RSclient)
* installing *source* package 'Rserve' ...
** using staged installation
checking whether to compile the server... yes
checking whether to compile the client... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking netinet/tcp.h usability... yes
checking netinet/tcp.h presence... yes
checking for netinet/tcp.h... yes
checking for an ANSI C-conforming const... yes
checking whether byte ordering is bigendian... no
checking whether time.h and sys/time.h may both be included... yes
checking for pid_t... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking for srandomdev... no
checking for library containing crypt... -lcrypt
checking crypt.h usability... yes
checking crypt.h presence... yes
checking for crypt.h... yes
checking for socklen_t... yes
checking for connect... yes
checking whether to enable IPv6... no
checking for dlopen in -ldl... yes
checking openssl/rsa.h usability... yes
checking openssl/rsa.h presence... yes
checking for openssl/rsa.h... yes
checking for library containing RSA_generate_key... -lcrypto
checking openssl/ssl.h usability... yes
checking openssl/ssl.h presence... yes
checking for openssl/ssl.h... yes
checking for library containing SSL_CTX_load_verify_locations... -lssl
checking whether threads are desired... yes
checking for working threads support... checking build system type... x86_64-pc-                                                                                                             linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking if compiler needs -Werror to reject unknown flags... no
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/client/cxx/Makefile
config.status: creating src/config.h
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c RSserver.c -o RSserver.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c Rserv.c -o Rserv.o
Rserv.c: In function 'generate_random_bytes':
Rserv.c:655:3: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarat                                                                                                             ions]
   RAND_pseudo_bytes(buf, len) == -1) {
   ^~~~~~~~~~~~~~~~~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from Rserv.c:651:
/usr/include/openssl/rand.h:44:1: note: declared here
 DEPRECATEDIN_1_1_0(int RAND_pseudo_bytes(unsigned char *buf, int num))
 ^
Rserv.c: In function 'rsa_gen_resp':
Rserv.c:2504:3: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarat                                                                                                             ions]
   rsa_srv_key = RSA_generate_key(4096, 65537, 0, 0);
   ^~~~~~~~~~~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from Rserv.c:651:
/usr/include/openssl/rsa.h:234:1: note: declared here
 DEPRECATEDIN_0_9_8(RSA *RSA_generate_key(int bits, unsigned long e, void
 ^
Rserv.c: In function 'performConfig':
Rserv.c:1035:4: warning: ignoring return value of 'setgid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
    setgid(ruid);
    ^~~~~~~~~~~~
Rserv.c:1036:3: warning: ignoring return value of 'setuid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
   setuid(ruid);
   ^~~~~~~~~~~~
Rserv.c:1039:22: warning: ignoring return value of 'setgid', declared with attri                                                                                                             bute warn_unused_result [-Wunused-result]
   if (requested_gid) setgid(requested_gid);
                      ^~~~~~~~~~~~~~~~~~~~~
Rserv.c:1040:22: warning: ignoring return value of 'setuid', declared with attri                                                                                                             bute warn_unused_result [-Wunused-result]
   if (requested_uid) setuid(requested_uid);
                      ^~~~~~~~~~~~~~~~~~~~~
Rserv.c: In function 'auth_user':
Rserv.c:2442:7: warning: ignoring return value of 'setgid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
       setgid(u_gid ? u_gid : default_gid);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Rserv.c:2444:7: warning: ignoring return value of 'setuid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
       setuid(u_uid ? u_uid : default_uid);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c http.c -o http.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c ioc.c -o ioc.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c md5.c -o md5.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c oc.c -o oc.o
oc.c: In function 'oc_new':
oc.c:50:5: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations                                                                                                             ]
     if (RAND_bytes(hash, 21) || RAND_pseudo_bytes(hash, 21))
     ^~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from oc.c:11:
/usr/include/openssl/rand.h:44:1: note: declared here
 DEPRECATEDIN_1_1_0(int RAND_pseudo_bytes(unsigned char *buf, int num))
 ^
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c qap_decode.c -o qap_decode.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c qap_encode.c -o qap_encode.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c rsio.c -o rsio.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c session.c -o session.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c sha1.c -o sha1.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c standalone.c -o standalone.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c tls.c -o tls.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c ulog.c -o ulog.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c utils.c -o utils.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c websockets.c -o websockets.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthrea                                                                                                             d  -I/usr/local/include  -fpic  -g -O2  -c winembed.c -o winembed.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o Rserve.so RSserver.o Rs                                                                                                             erv.o base64.o http.o ioc.o md5.o oc.o qap_decode.o qap_encode.o rsio.o session.                                                                                                             o sha1.o standalone.o tls.o ulog.o utils.o websockets.o winembed.o -lssl -lcrypt                                                                                                             o -ldl -lcrypt -L/opt/R/3.6.1/lib/R/lib -lR
gcc -DSTANDALONE_RSERVE -DDAEMON -I. -Iinclude -I"/opt/R/3.6.1/lib/R/include" -D                                                                                                             NDEBUG -DRSERVE_PKG -I. -Iinclude   -pthread  -I/usr/local/include  -fpic  -g -O                                                                                                             2  -I/usr/local/include -g -O2  -DRSERVE_PKG -I. -Iinclude   -pthread  -o Rserve                                                                                                              standalone.c md5.c session.c qap_decode.c qap_encode.c sha1.c base64.c websocke                                                                                                             ts.c RSserver.c tls.c http.c oc.c rsio.c ulog.c ioc.c utils.c -lssl -lcrypto -ld                                                                                                             l -lcrypt    -L"/opt/R/3.6.1/lib/R/lib" -lR -lssl -lcrypto -ldl -lcrypt
In file included from standalone.c:6:0:
Rserv.c: In function 'generate_random_bytes':
Rserv.c:655:3: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarat                                                                                                             ions]
   RAND_pseudo_bytes(buf, len) == -1) {
   ^~~~~~~~~~~~~~~~~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from Rserv.c:651,
                 from standalone.c:6:
/usr/include/openssl/rand.h:44:1: note: declared here
 DEPRECATEDIN_1_1_0(int RAND_pseudo_bytes(unsigned char *buf, int num))
 ^
In file included from standalone.c:6:0:
Rserv.c: In function 'rsa_gen_resp':
Rserv.c:2504:3: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarat                                                                                                             ions]
   rsa_srv_key = RSA_generate_key(4096, 65537, 0, 0);
   ^~~~~~~~~~~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from Rserv.c:651,
                 from standalone.c:6:
/usr/include/openssl/rsa.h:234:1: note: declared here
 DEPRECATEDIN_0_9_8(RSA *RSA_generate_key(int bits, unsigned long e, void
 ^
In file included from standalone.c:6:0:
Rserv.c: In function 'performConfig':
Rserv.c:1035:4: warning: ignoring return value of 'setgid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
    setgid(ruid);
    ^~~~~~~~~~~~
Rserv.c:1036:3: warning: ignoring return value of 'setuid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
   setuid(ruid);
   ^~~~~~~~~~~~
Rserv.c:1039:22: warning: ignoring return value of 'setgid', declared with attri                                                                                                             bute warn_unused_result [-Wunused-result]
   if (requested_gid) setgid(requested_gid);
                      ^~~~~~~~~~~~~~~~~~~~~
Rserv.c:1040:22: warning: ignoring return value of 'setuid', declared with attri                                                                                                             bute warn_unused_result [-Wunused-result]
   if (requested_uid) setuid(requested_uid);
                      ^~~~~~~~~~~~~~~~~~~~~
Rserv.c: In function 'auth_user':
Rserv.c:2442:7: warning: ignoring return value of 'setgid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
       setgid(u_gid ? u_gid : default_gid);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Rserv.c:2444:7: warning: ignoring return value of 'setuid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
       setuid(u_uid ? u_uid : default_uid);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
oc.c: In function 'oc_new':
oc.c:50:5: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations                                                                                                             ]
     if (RAND_bytes(hash, 21) || RAND_pseudo_bytes(hash, 21))
     ^~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from oc.c:11:
/usr/include/openssl/rand.h:44:1: note: declared here
 DEPRECATEDIN_1_1_0(int RAND_pseudo_bytes(unsigned char *buf, int num))
 ^
gcc -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude -I"/opt/R/3.6.1/l                                                                                                             ib/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude   -pthread  -I/usr/local/inclu                                                                                                             de  -fpic  -g -O2  -DRSERVE_PKG -I. -Iinclude   -pthread  -o Rserve.dbg standalo                                                                                                             ne.c md5.c session.c qap_decode.c qap_encode.c sha1.c base64.c websockets.c RSse                                                                                                             rver.c tls.c http.c oc.c rsio.c ulog.c ioc.c utils.c -lssl -lcrypto -ldl -lcrypt                                                                                                                 -L"/opt/R/3.6.1/lib/R/lib" -lR -lssl -lcrypto -ldl -lcrypt
In file included from standalone.c:6:0:
Rserv.c: In function 'generate_random_bytes':
Rserv.c:655:3: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarat                                                                                                             ions]
   RAND_pseudo_bytes(buf, len) == -1) {
   ^~~~~~~~~~~~~~~~~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from Rserv.c:651,
                 from standalone.c:6:
/usr/include/openssl/rand.h:44:1: note: declared here
 DEPRECATEDIN_1_1_0(int RAND_pseudo_bytes(unsigned char *buf, int num))
 ^
In file included from standalone.c:6:0:
Rserv.c: In function 'rsa_gen_resp':
Rserv.c:2504:3: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarat                                                                                                             ions]
   rsa_srv_key = RSA_generate_key(4096, 65537, 0, 0);
   ^~~~~~~~~~~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from Rserv.c:651,
                 from standalone.c:6:
/usr/include/openssl/rsa.h:234:1: note: declared here
 DEPRECATEDIN_0_9_8(RSA *RSA_generate_key(int bits, unsigned long e, void
 ^
In file included from standalone.c:6:0:
Rserv.c: In function 'performConfig':
Rserv.c:1035:4: warning: ignoring return value of 'setgid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
    setgid(ruid);
    ^~~~~~~~~~~~
Rserv.c:1036:3: warning: ignoring return value of 'setuid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
   setuid(ruid);
   ^~~~~~~~~~~~
Rserv.c:1039:22: warning: ignoring return value of 'setgid', declared with attri                                                                                                             bute warn_unused_result [-Wunused-result]
   if (requested_gid) setgid(requested_gid);
                      ^~~~~~~~~~~~~~~~~~~~~
Rserv.c:1040:22: warning: ignoring return value of 'setuid', declared with attri                                                                                                             bute warn_unused_result [-Wunused-result]
   if (requested_uid) setuid(requested_uid);
                      ^~~~~~~~~~~~~~~~~~~~~
Rserv.c: In function 'auth_user':
Rserv.c:2442:7: warning: ignoring return value of 'setgid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
       setgid(u_gid ? u_gid : default_gid);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Rserv.c:2444:7: warning: ignoring return value of 'setuid', declared with attrib                                                                                                             ute warn_unused_result [-Wunused-result]
       setuid(u_uid ? u_uid : default_uid);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
oc.c: In function 'oc_new':
oc.c:50:5: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations                                                                                                             ]
     if (RAND_bytes(hash, 21) || RAND_pseudo_bytes(hash, 21))
     ^~
In file included from /usr/include/openssl/e_os2.h:13:0,
                 from /usr/include/openssl/ossl_typ.h:19,
                 from /usr/include/openssl/rand.h:14,
                 from oc.c:11:
/usr/include/openssl/rand.h:44:1: note: declared here
 DEPRECATEDIN_1_1_0(int RAND_pseudo_bytes(unsigned char *buf, int num))
 ^
./mergefat Rserve "/opt/R/3.6.1/lib/R/bin/Rserve"
./mergefat Rserve.dbg "/opt/R/3.6.1/lib/R/bin/Rserve.dbg"
make -C proxy 'CC=gcc' 'CPPFLAGS=-I.. -DFORKED -I/usr/local/include -DRSERVE_PKG                                                                                                              -I. -Iinclude   -pthread' CFLAGS='-g -O2   -pthread' 'LIBS=-lssl -lcrypto -ldl                                                                                                              -lcrypt  ' && cp -p proxy/forward .
make[1]: Entering directory '/tmp/RtmpsqAT7G/R.INSTALL10cd5569890f/Rserve/src/pr                                                                                                             oxy'
ln -sfn ../ulog.h ulog.h
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o forward.o forward.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o http.o http.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o http_tools.o http_tools.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o server.o server.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o tls.o tls.c
ln -sfn ../md5.h md5.h
ln -sfn ../sha1.h sha1.h
ln -sfn ../base64.c base64.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o websockets.o websockets.c
ln -sfn ../md5.c md5.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o md5.o md5.c
ln -sfn ../sha1.c sha1.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o sha1.o sha1.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o base64.o base64.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o date.o date.c
ln -sfn ../ulog.c ulog.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o ulog.o ulog.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o chandler.o chandler.c
gcc -g -O2   -pthread -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iincl                                                                                                             ude   -pthread  -c -o rscript.o rscript.c
gcc -g -O2   -pthread  -o forward forward.o http.o http_tools.o server.o tls.o w                                                                                                             ebsockets.o md5.o sha1.o base64.o date.o ulog.o chandler.o rscript.o -lssl -lcry                                                                                                             pto -ldl -lcrypt   -lssl
make[1]: Leaving directory '/tmp/RtmpsqAT7G/R.INSTALL10cd5569890f/Rserve/src/pro                                                                                                             xy'
installing via 'install.libs.R' to /opt/R/3.6.1/lib/R/library/00LOCK-Rserve/00ne                                                                                                             w/Rserve
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rserve)
* installing *source* package 'base64enc' ...
** using staged installation
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c base64.c -o base64.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c uriencode.c -o uriencode.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c utf8.c -o utf8.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o base64enc.so base64.o u                                                                                                             riencode.o utf8.o -L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-base64enc/00new/base64enc/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (base64enc)
* installing *source* package 'uuid' ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking for stdlib.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/sockio.h usability... no
checking sys/sockio.h presence... no
checking for sys/sockio.h... no
checking sys/syscall.h usability... yes
checking sys/syscall.h presence... yes
checking for sys/syscall.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking for unistd.h... (cached) yes
checking for net/if.h... yes
checking for net/if_dl.h... no
checking for jrand48... yes
checking for flock... yes
checking for struct sockaddr.sa_len... no
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c R.c -o R.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c clear.c -o clear.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c compare.c -o compare.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c copy.c -o copy.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c gen_uuid.c -o gen_uuid.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c isnull.c -o isnull.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c pack.c -o pack.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c parse.c -o parse.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c unpack.c -o unpack.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/i                                                                                                             nclude  -fpic  -g -O2  -c unparse.c -o unparse.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o uuid.so R.o clear.o com                                                                                                             pare.o copy.o gen_uuid.o isnull.o pack.o parse.o unpack.o unparse.o -L/opt/R/3.6                                                                                                             .1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-uuid/00new/uuid/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (uuid)
* installing *source* package 'unixtools' ...
** using staged installation
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c settemp.c -o settemp.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c stack.c -o stack.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c unix.c -o unix.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o unixtools.so settemp.o                                                                                                              stack.o unix.o -L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-unixtools/00new/unixtools/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (unixtools)
* installing *source* package 'rediscc' ...
** using staged installation
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c async.c -o async.o
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33:                                                                                                             0,
                 from /usr/include/stdlib.h:25,
                 from async.c:33:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE a                                                                                                             re deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c credis.c -o credis.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c dict.c -o dict.o
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33:                                                                                                             0,
                 from /usr/include/stdlib.h:25,
                 from dict.c:37:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE a                                                                                                             re deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c hiredis.c -o hiredis.o
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33:                                                                                                             0,
                 from /usr/include/string.h:26,
                 from hiredis.c:33:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE a                                                                                                             re deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c net.c -o net.o
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25:0,
                 from net.c:34:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE a                                                                                                             re deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c sds.c -o sds.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o rediscc.so async.o cred                                                                                                             is.o dict.o hiredis.o net.o sds.o -L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-rediscc/00new/rediscc/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rediscc)
* installing *source* package 'png' ...
** using staged installation
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  `libpng-conf                                                                                                             ig --cflags` -fpic  -g -O2  -c read.c -o read.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  `libpng-conf                                                                                                             ig --cflags` -fpic  -g -O2  -c write.c -o write.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o png.so read.o write.o -                                                                                                             lpng16 -lm -lz -lm -L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-png/00new/png/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (png)
* installing *source* package 'Cairo' ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for pkg-config... /usr/bin/pkg-config
checking whether pkg-config knows about cairo... yes
checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-p                                                                                                             s cairo-xlib cairo-xlib-xrender
configure: CAIRO_CFLAGS=-I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/                                                                                                             x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetyp                                                                                                             e2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/libpng16
checking if R was compiled with the RConn patch... no
checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
checking for ATS font support in Cairo... no
configure: CAIRO_LIBS=-lfreetype -lz -lpng16 -lz -lcairo -lXext -lXrender -lX11
checking for library containing deflate... none required
checking whether Cairo programs can be compiled... yes
checking whether cairo_image_surface_get_format is declared... no
checking for FreeType support in cairo... yes
checking whether FreeType needs additional flags... no
checking wheter libjpeg works... yes
checking wheter libtiff works... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/cconfig.h
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c ca                                                                                                             irobem.c -o cairobem.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c ca                                                                                                             irogd.c -o cairogd.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c ca                                                                                                             irotalk.c -o cairotalk.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c im                                                                                                             g-backend.c -o img-backend.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c im                                                                                                             g-jpeg.c -o img-jpeg.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c im                                                                                                             g-tiff.c -o img-tiff.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c pd                                                                                                             f-backend.c -o pdf-backend.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c ps                                                                                                             -backend.c -o ps-backend.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c sv                                                                                                             g-backend.c -o svg-backend.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c w3                                                                                                             2-backend.c -o w32-backend.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/                                                                                                             glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I                                                                                                             /usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/i                                                                                                             nclude/libpng16  -I. -Iinclude  -I/usr/local/include -g -O2 -fpic  -g -O2  -c xl                                                                                                             ib-backend.c -o xlib-backend.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o Cairo.so cairobem.o cai                                                                                                             rogd.o cairotalk.o img-backend.o img-jpeg.o img-tiff.o pdf-backend.o ps-backend.                                                                                                             o svg-backend.o w32-backend.o xlib-backend.o -lfreetype -lz -lpng16 -lz -lcairo                                                                                                              -lXext -lXrender -lX11 -ljpeg -ltiff -L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-Cairo/00new/Cairo/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Cairo)
* installing *source* package 'mime' ...
** using staged installation
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c init.c -o init.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c rawmatch.c -o rawmatch.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o mime.so init.o rawmatch                                                                                                             .o -L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-mime/00new/mime/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mime)
* installing *source* package 'gist' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'gist'
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gist)
* installing *source* package 'rcloud.sh' ...
** using staged installation
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c shexec.c -o shexec.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o rcloud.sh.so shexec.o -                                                                                                             L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-rcloud.sh/00new/rcloud.sh/libs
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'rcloud.sh'
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rcloud.sh)
* installing *source* package 'PKI' ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking openssl/ssl.h usability... yes
checking openssl/ssl.h presence... yes
checking for openssl/ssl.h... yes
checking openssl/rsa.h usability... yes
checking openssl/rsa.h presence... yes
checking for openssl/rsa.h... yes
checking for library containing RSA_generate_key_ex... -lcrypto
checking for openssl/ssl.h... (cached) yes
checking for library containing SSL_CTX_load_verify_locations... -lssl
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c asn1.c -o asn1.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c init.c -o init.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c pki-x509.c -o pki-x509.o
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O                                                                                                             2  -c tools.c -o tools.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o PKI.so asn1.o init.o pk                                                                                                             i-x509.o tools.o -lssl -lcrypto -L/opt/R/3.6.1/lib/R/lib -lR
installing to /opt/R/3.6.1/lib/R/library/00LOCK-PKI/00new/PKI/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PKI)
* installing *source* package 'FastRWeb' ...
** using staged installation
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking netinet/tcp.h usability... yes
checking netinet/tcp.h presence... yes
checking for netinet/tcp.h... yes
checking for an ANSI C-conforming const... yes
checking whether byte ordering is bigendian... no
checking whether time.h and sys/time.h may both be included... yes
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking for library containing crypt... -lcrypt
checking crypt.h usability... yes
checking crypt.h presence... yes
checking for crypt.h... yes
checking for socklen_t... yes
checking for connect... yes
configure: creating ./config.status
config.status: creating src/Rcgi/Makefile
config.status: creating src/Rcgi/config.h
** libs
** arch -
compiling Rcgi
make[1]: Entering directory '/tmp/Rtmp0Ywy7g/R.INSTALL23a57bed19f4/FastRWeb/src/                                                                                                             Rcgi'
g++  -DHAVE_CONFIG_H -I.   -c -o Rconnection.o Rconnection.cc
In file included from Rconnection.cc:27:0:
Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)':
Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to '                                                                                                             char*' [-Wwrite-strings]
     { name=""; fix_content(); }
            ^~
Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)':
Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to '                                                                                                             char*' [-Wwrite-strings]
     { name=""; fix_content(); }
            ^~
Rconnection.cc: At global scope:
Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to '                                                                                                             char*' [-Wwrite-strings]
 static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol versi                                                                                                             on 0103 */
                    ^~~~~~~~~~~~~~
g++  -DHAVE_CONFIG_H -I.   -c -o Rcgi.o Rcgi.cc
In file included from Rcgi.cc:94:0:
Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)':
Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to '                                                                                                             char*' [-Wwrite-strings]
     { name=""; fix_content(); }
            ^~
Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)':
Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to '                                                                                                             char*' [-Wwrite-strings]
     { name=""; fix_content(); }
            ^~
g++ Rconnection.o Rcgi.o -o Rcgi -lcrypt
make[1]: Leaving directory '/tmp/Rtmp0Ywy7g/R.INSTALL23a57bed19f4/FastRWeb/src/R                                                                                                             cgi'
rm -rf ../inst/Rcgi
cp -r Rcgi ../inst
mkdir ../inst/cgi-bin
touch null.so null.dll # to make R CMD SHLIB happy
installing to /opt/R/3.6.1/lib/R/library/00LOCK-FastRWeb/00new/FastRWeb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FastRWeb)
ERROR: dependency 'xfun' is not available for package 'markdown'
* removing '/opt/R/3.6.1/lib/R/library/markdown'
ERROR: dependencies 'github', 'httr' are not available for package 'githubgist'
* removing '/opt/R/3.6.1/lib/R/library/githubgist'
* installing *source* package 'rcloud.web' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning in value[[3L]](cond) :
  NOTE: rcloud.web can only be used in an RCloud session!
** testing if installed package can be loaded from final location
Warning in value[[3L]](cond) :
  NOTE: rcloud.web can only be used in an RCloud session!
** testing if installed package keeps a record of temporary installation path
* DONE (rcloud.web)
ERROR: dependencies 'markdown', 'stringr', 'yaml' are not available for package                                                                                                              'knitr'
* removing '/opt/R/3.6.1/lib/R/library/knitr'
ERROR: dependencies 'Rcpp', 'guitar' are not available for package 'gitgist'
* removing '/opt/R/3.6.1/lib/R/library/gitgist'
* installing *source* package 'rcloud.client' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'rcloud.client'
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rcloud.client)
ERROR: dependencies 'knitr', 'markdown', 'reticulate', 'jsonlite' are not availa                                                                                                             ble for package 'rcloud.jupyter'
* removing '/opt/R/3.6.1/lib/R/library/rcloud.jupyter'
ERROR: dependencies 'knitr', 'markdown' are not available for package 'rcloud.py                                                                                                             thon'
* removing '/opt/R/3.6.1/lib/R/library/rcloud.python'
ERROR: dependencies 'knitr', 'markdown' are not available for package 'rcloud.r'
* removing '/opt/R/3.6.1/lib/R/library/rcloud.r'
ERROR: dependencies 'knitr', 'rmarkdown' are not available for package 'rcloud.r                                                                                                             markdown'
* removing '/opt/R/3.6.1/lib/R/library/rcloud.rmarkdown'
ERROR: dependencies 'rjson', 'RCurl', 'jsonlite', 'knitr', 'markdown', 'httr', '                                                                                                             sendmailR' are not available for package 'rcloud.support'
* removing '/opt/R/3.6.1/lib/R/library/rcloud.support'
ERROR: dependency 'rcloud.support' is not available for package 'rcloud.enviewer                                                                                                             '
* removing '/opt/R/3.6.1/lib/R/library/rcloud.enviewer'
ERROR: dependency 'rcloud.support' is not available for package 'rcloud.lux'
* removing '/opt/R/3.6.1/lib/R/library/rcloud.lux'
ERROR: dependency 'rcloud.support' is not available for package 'rcloud.notebook                                                                                                             .info'
* removing '/opt/R/3.6.1/lib/R/library/rcloud.notebook.info'
ERROR: dependency 'rcloud.support' is not available for package 'rcloud.viewer'
* removing '/opt/R/3.6.1/lib/R/library/rcloud.viewer'

The downloaded source packages are in
        '/tmp/RtmpJudbGV/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
There were 15 warnings (use warnings() to see them)
Error in library(rcloud.support) :
  there is no package called 'rcloud.support'
Execution halted

 ERROR: one or more packages could not be installed.
 Please check that you have all necessary dependencies installed

The command '/bin/sh -c apt-get install -y gcc g++ gfortran libcairo-dev libread                                                                                                             line-dev libxt-dev libjpeg-dev     libicu-dev libssl-dev libcurl4-openssl-dev su
gordonwoodhull commented 4 years ago

Hi @sunny143code, I think that CRAN mirror no longer exists.

Could you please try replacing all instances of r.research.att.com in scripts/bootstrap.R with a CRAN mirror near to you, from those listed at

https://cran.r-project.org/ ?

If this is the problem, I think we will need to change all of the following.

@s-u, is there a generic CRAN server we should use?

$ grep -rl r.research.att.com .
./docker/rcloud.conf
./Dockerfile
./rcloud.support/R/install.R
./scripts/bootstrapR.sh
./conf/solr/solrsetup.sh
./conf/run_rcloud.R
s-u commented 4 years ago

Should be fixed now. What happened is that R.research has now different IPs inside and outside so the outside one wan't setup as a mirror. I have added a redirect to CRAN CDN:https://cloud.R-project.org (which is the answer to your other question).

gordonwoodhull commented 4 years ago

Thanks @s-u!! Much better solution.

sunny143code commented 4 years ago

Thanks a lot for the quick response. I will try again the process for the installation of app and let you know how it goes.

gordonwoodhull commented 4 years ago

Closing this. @sunny143code, please comment if this issue is not resolved.

(Doubtless you'll have other installation questions, but I think @s-u resolved the issue with r.research.att.com.)